Next Generation sequencing (NGS) methods typically generate millions of “reads” that originate from individual molecules of DNA. Some methods, such as nanopore sequencing methods or Pacific Biosciences SMRT technology, report sequence information from individual single molecules of DNA. However, it can be difficult to achieve suitable signal to noise ratios with single molecules, making it difficult to distinguish biological sequence changes from errors. Therefore, a number of NGS platforms such as 454, Illumina, and SOLID use a method of “clonal amplification” to generate many identical copies of individual DNA molecules. These copies are segregated in individual “clusters,” or on beads, which were seeded by an individual DNA molecule. Sequencing reactions proceed on the identical copies in parallel, multiplying the signal.
Generally speaking, the clonal amplification methods fall into two classes: bead based, and surface based. Bead based methods often involve emulsion PCR, for example as commercialized by 454 and Ion Torrent technologies. Examples of surface based amplification methods include the “bridge amplification” method commercialized by Illumina and the “wildfire” or “avalanche” method described by Life Technologies. Due to technical difficulties of working with micron sized beads (clogging, enrichment of beads with DNA attached, packing uniformity), higher surface densities of amplified DNA colonies on a flow cell can generally be achieved using surface amplification methods.
Among other things, the present disclosure provides a way to amplify DNA. The method can be used to amplify DNA molecules in solution or on the surface of a support. In some embodiments, amplification may result a “cluster” of amplification products that can be sequenced by any convenient method.